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450 | class IndexCrystFELParameters(ThirdPartyParameters):
"""Parameters for CrystFEL's `indexamajig`.
There are many parameters, and many combinations. For more information on
usage, please refer to the CrystFEL documentation, here:
https://www.desy.de/~twhite/crystfel/manual-indexamajig.html
"""
class Config(ThirdPartyParameters.Config):
set_result: bool = True
"""Whether the Executor should mark a specified parameter as a result."""
long_flags_use_eq: bool = True
"""Whether long command-line arguments are passed like `--long=arg`."""
executable: str = Field(
"/sdf/group/lcls/ds/tools/crystfel/0.10.2/bin/indexamajig",
description="CrystFEL's indexing binary.",
flag_type="",
)
# Basic options
in_file: Optional[str] = Field(
"", description="Path to input file.", flag_type="-", rename_param="i"
)
out_file: str = Field(
"",
description="Path to output file.",
flag_type="-",
rename_param="o",
is_result=True,
)
peaks: Optional[str] = Field(
None,
description=(
"Peak finding algorithm, or file type. E.g. peakfinder8 to peak find, "
"or use cxi for CXI files."
),
flag_type="--",
)
geometry: str = Field(
"", description="Path to geometry file.", flag_type="-", rename_param="g"
)
zmq_input: Optional[str] = Field(
description="ZMQ address to receive data over. `input` and `zmq-input` are mutually exclusive",
flag_type="--",
rename_param="zmq-input",
)
zmq_subscribe: Optional[str] = Field( # Can be used multiple times...
description="Subscribe to ZMQ message of type `tag`",
flag_type="--",
rename_param="zmq-subscribe",
)
zmq_request: Optional[AnyUrl] = Field(
description="Request new data over ZMQ by sending this value",
flag_type="--",
rename_param="zmq-request",
)
asapo_endpoint: Optional[str] = Field(
description="ASAP::O endpoint. zmq-input and this are mutually exclusive.",
flag_type="--",
rename_param="asapo-endpoint",
)
asapo_token: Optional[str] = Field(
description="ASAP::O authentication token.",
flag_type="--",
rename_param="asapo-token",
)
asapo_beamtime: Optional[str] = Field(
description="ASAP::O beatime.",
flag_type="--",
rename_param="asapo-beamtime",
)
asapo_source: Optional[str] = Field(
description="ASAP::O data source.",
flag_type="--",
rename_param="asapo-source",
)
asapo_group: Optional[str] = Field(
description="ASAP::O consumer group.",
flag_type="--",
rename_param="asapo-group",
)
asapo_stream: Optional[str] = Field(
description="ASAP::O stream.",
flag_type="--",
rename_param="asapo-stream",
)
asapo_wait_for_stream: Optional[str] = Field(
description="If ASAP::O stream does not exist, wait for it to appear.",
flag_type="--",
rename_param="asapo-wait-for-stream",
)
data_format: Optional[str] = Field(
description="Specify format for ZMQ or ASAP::O. `msgpack`, `hdf5` or `seedee`.",
flag_type="--",
rename_param="data-format",
)
basename: bool = Field(
False,
description="Remove directory parts of filenames. Acts before prefix if prefix also given.",
flag_type="--",
)
prefix: Optional[str] = Field(
description="Add a prefix to the filenames from the infile argument.",
flag_type="--",
rename_param="asapo-stream",
)
nthreads: PositiveInt = Field(
max(int(os.environ.get("SLURM_NPROCS", len(os.sched_getaffinity(0)))) - 1, 1),
description="Number of threads to use. See also `max_indexer_threads`.",
flag_type="-",
rename_param="j",
)
no_check_prefix: bool = Field(
False,
description="Don't attempt to correct the prefix if it seems incorrect.",
flag_type="--",
rename_param="no-check-prefix",
)
highres: Optional[float] = Field(
description="Mark all pixels greater than `x` has bad.", flag_type="--"
)
profile: bool = Field(
False, description="Display timing data to monitor performance.", flag_type="--"
)
temp_dir: Optional[str] = Field(
description="Specify a path for the temp files folder.",
flag_type="--",
rename_param="temp-dir",
)
wait_for_file: conint(gt=-2) = Field( # type: ignore
0,
description="Wait at most `x` seconds for a file to be created. A value of -1 means wait forever.",
flag_type="--",
rename_param="wait-for-file",
)
no_image_data: bool = Field(
False,
description="Load only the metadata, no iamges. Can check indexability without high data requirements.",
flag_type="--",
rename_param="no-image-data",
)
# Peak-finding options
# ....
# Indexing options
indexing: Optional[str] = Field(
description="Comma-separated list of supported indexing algorithms to use. Default is to automatically detect.",
flag_type="--",
)
cell_file: Optional[str] = Field(
description="Path to a file containing unit cell information (PDB or CrystFEL format).",
flag_type="-",
rename_param="p",
)
tolerance: str = Field(
"5,5,5,1.5",
description=(
"Tolerances (in percent) for unit cell comparison. "
"Comma-separated list a,b,c,angle. Default=5,5,5,1.5"
),
flag_type="--",
)
no_check_cell: bool = Field(
False,
description="Do not check cell parameters against unit cell. Replaces '-raw' method.",
flag_type="--",
rename_param="no-check-cell",
)
no_check_peaks: bool = Field(
False,
description="Do not verify peaks are accounted for by solution.",
flag_type="--",
rename_param="no-check-peaks",
)
multi: bool = Field(
False, description="Enable multi-lattice indexing.", flag_type="--"
)
wavelength_estimate: Optional[float] = Field(
description="Estimate for X-ray wavelength. Required for some methods.",
flag_type="--",
rename_param="wavelength-estimate",
)
camera_length_estimate: Optional[float] = Field(
description="Estimate for camera distance. Required for some methods.",
flag_type="--",
rename_param="camera-length-estimate",
)
max_indexer_threads: Optional[PositiveInt] = Field(
# 1,
description="Some indexing algos can use multiple threads. In addition to image-based.",
flag_type="--",
rename_param="max-indexer-threads",
)
no_retry: bool = Field(
False,
description="Do not remove weak peaks and try again.",
flag_type="--",
rename_param="no-retry",
)
no_refine: bool = Field(
False,
description="Skip refinement step.",
flag_type="--",
rename_param="no-refine",
)
no_revalidate: bool = Field(
False,
description="Skip revalidation step.",
flag_type="--",
rename_param="no-revalidate",
)
# TakeTwo specific parameters
taketwo_member_threshold: Optional[PositiveInt] = Field(
# 20,
description="Minimum number of vectors to consider.",
flag_type="--",
rename_param="taketwo-member-threshold",
)
taketwo_len_tolerance: Optional[PositiveFloat] = Field(
# 0.001,
description="TakeTwo length tolerance in Angstroms.",
flag_type="--",
rename_param="taketwo-len-tolerance",
)
taketwo_angle_tolerance: Optional[PositiveFloat] = Field(
# 0.6,
description="TakeTwo angle tolerance in degrees.",
flag_type="--",
rename_param="taketwo-angle-tolerance",
)
taketwo_trace_tolerance: Optional[PositiveFloat] = Field(
# 3,
description="Matrix trace tolerance in degrees.",
flag_type="--",
rename_param="taketwo-trace-tolerance",
)
# Felix-specific parameters
# felix_domega
# felix-fraction-max-visits
# felix-max-internal-angle
# felix-max-uniqueness
# felix-min-completeness
# felix-min-visits
# felix-num-voxels
# felix-sigma
# felix-tthrange-max
# felix-tthrange-min
# XGANDALF-specific parameters
xgandalf_sampling_pitch: Optional[NonNegativeInt] = Field(
# 6,
description="Density of reciprocal space sampling.",
flag_type="--",
rename_param="xgandalf-sampling-pitch",
)
xgandalf_grad_desc_iterations: Optional[NonNegativeInt] = Field(
# 4,
description="Number of gradient descent iterations.",
flag_type="--",
rename_param="xgandalf-grad-desc-iterations",
)
xgandalf_tolerance: Optional[PositiveFloat] = Field(
# 0.02,
description="Relative tolerance of lattice vectors",
flag_type="--",
rename_param="xgandalf-tolerance",
)
xgandalf_no_deviation_from_provided_cell: Optional[bool] = Field(
description="Found unit cell must match provided.",
flag_type="--",
rename_param="xgandalf-no-deviation-from-provided-cell",
)
xgandalf_min_lattice_vector_length: Optional[PositiveFloat] = Field(
# 30,
description="Minimum possible lattice length.",
flag_type="--",
rename_param="xgandalf-min-lattice-vector-length",
)
xgandalf_max_lattice_vector_length: Optional[PositiveFloat] = Field(
# 250,
description="Minimum possible lattice length.",
flag_type="--",
rename_param="xgandalf-max-lattice-vector-length",
)
xgandalf_max_peaks: Optional[PositiveInt] = Field(
# 250,
description="Maximum number of peaks to use for indexing.",
flag_type="--",
rename_param="xgandalf-max-peaks",
)
xgandalf_fast_execution: bool = Field(
False,
description="Shortcut to set sampling-pitch=2, and grad-desc-iterations=3.",
flag_type="--",
rename_param="xgandalf-fast-execution",
)
# pinkIndexer parameters
# ...
# asdf_fast: bool = Field(False, description="Enable fast mode for asdf. 3x faster for 7% loss in accuracy.", flag_type="--", rename_param="asdf-fast")
# Integration parameters
integration: str = Field(
"rings-nocen", description="Method for integrating reflections.", flag_type="--"
)
fix_profile_radius: Optional[float] = Field(
description="Fix the profile radius (m^{-1})",
flag_type="--",
rename_param="fix-profile-radius",
)
fix_divergence: Optional[float] = Field(
0,
description="Fix the divergence (rad, full angle).",
flag_type="--",
rename_param="fix-divergence",
)
int_radius: str = Field(
"4,5,7",
description="Inner, middle, and outer radii for 3-ring integration.",
flag_type="--",
rename_param="int-radius",
)
int_diag: str = Field(
"none",
description="Show detailed information on integration when condition is met.",
flag_type="--",
rename_param="int-diag",
)
push_res: str = Field(
"infinity",
description="Integrate `x` higher than apparent resolution limit (nm-1).",
flag_type="--",
rename_param="push-res",
)
overpredict: bool = Field(
False,
description="Over-predict reflections. Maybe useful with post-refinement.",
flag_type="--",
)
cell_parameters_only: bool = Field(
False, description="Do not predict refletions at all", flag_type="--"
)
# Output parameters
no_non_hits_in_stream: bool = Field(
False,
description="Exclude non-hits from the stream file.",
flag_type="--",
rename_param="no-non-hits-in-stream",
)
copy_hheader: Optional[str] = Field(
description="Copy information from header in the image to output stream.",
flag_type="--",
rename_param="copy-hheader",
)
no_peaks_in_stream: bool = Field(
False,
description="Do not record peaks in stream file.",
flag_type="--",
rename_param="no-peaks-in-stream",
)
no_refls_in_stream: bool = Field(
False,
description="Do not record reflections in stream.",
flag_type="--",
rename_param="no-refls-in-stream",
)
serial_offset: Optional[PositiveInt] = Field(
description="Start numbering at `x` instead of 1.",
flag_type="--",
rename_param="serial-offset",
)
harvest_file: Optional[str] = Field(
description="Write parameters to file in JSON format.",
flag_type="--",
rename_param="harvest-file",
)
@validator("in_file", always=True)
def validate_in_file(cls, in_file: str, values: Dict[str, Any]) -> str:
if in_file == "":
filename: Optional[str] = read_latest_db_entry(
f"{values['lute_config'].work_dir}", "FindPeaksPyAlgos", "out_file"
)
if filename is None:
exp: str = values["lute_config"].experiment
run: int = int(values["lute_config"].run)
tag: Optional[str] = read_latest_db_entry(
f"{values['lute_config'].work_dir}", "FindPeaksPsocake", "tag"
)
out_dir: Optional[str] = read_latest_db_entry(
f"{values['lute_config'].work_dir}", "FindPeaksPsocake", "outDir"
)
if out_dir is not None:
fname: str = f"{out_dir}/{exp}_{run:04d}"
if tag is not None:
fname = f"{fname}_{tag}"
return f"{fname}.lst"
else:
return filename
return in_file
@validator("out_file", always=True)
def validate_out_file(cls, out_file: str, values: Dict[str, Any]) -> str:
if out_file == "":
expmt: str = values["lute_config"].experiment
run: int = int(values["lute_config"].run)
work_dir: str = values["lute_config"].work_dir
tag: Optional[str] = read_latest_db_entry(
f"{values['lute_config'].work_dir}", "FindPeaksPyAlgos", "tag"
)
if tag is None:
tag = read_latest_db_entry(
f"{values['lute_config'].work_dir}", "FindPeaksPsocake", "tag"
)
fname: str = f"{expmt}_r{run:04d}"
if tag is not None:
fname = f"{fname}_{tag}"
return f"{work_dir}/{fname}.stream"
return out_file
|